uvmggfandomcom-20200215-history
UVM Genetics
Welcome to the UVM Genetics & Genomics Wiki Class wiki for the Genetics and Genomics course in the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington VT USA. John Burke is the course instructor, and can be reached at john.burke@uvm.edu or @JohnBTV. The Twitter hashtag for the course is #uvmgg. Comments, questions and suggestions are welcome. Use the comments section on the relevant page, or John's Wikia wall, or Twitter as appropriate. About the Course This course is being offered for the first time in the 2012 fall semester, and is intended for both graduate students and advanced undergraduates. It will be a highly collaborative and open course in which students will have the backing of an excellent textbook and an experienced instructor, while learning how to cope with a vast flow of new information. Students will generate, evaluate, and collaboratively edit content and will primarily be evaluated by the quality of their contributions and collaborations in class and on this wiki. Getting Started #Sign up for the course and pay your tuition bill. (Thanks, mom!). Of course, auditors and visitors are also welcome. #The class will be held in Stafford 301, Monday and Wednesday from 5:30 - 6:45 PM. Note that the location differs from that listed by the registrar's office. #Get your hands on a copy of the textbook, Introduction to Genomics (Oxford University Press, 2nd edition, 2012, ISBN 9780199564354),'' by Arthur M Lesk. The UVM bookstore is having trouble acquiring them, so I recommend getting a copy through your favorite online bookseller. As of this writing, copies are available from Amazon (http://amzn.to/QaiESD), Barnes & Noble (http://bit.ly/PH8cON) and a variety of other suppliers (http://bit.ly/QakqDm). The textbook is excellent, fun to read, moderately priced ($55-$75), and we'll make good use of it. You might be able to get by without your own copy, but I really do not recommend trying to do so. No need to pay for expedited shipping, as I have made pdfs of the first three chapters, and will provide them to the class. #I strongly recommend bringing a laptop to class for web access and wiki editing. Alternatively, a tablet or smartphone may be used, if you are comfortable editing on smaller devices. It does not matter if you use a PC, Mac, Linux, Android, or iOS device, since we will only use universal software, most of which is cloud-based. #Download and install Evernote(free) on all of your devices. Evernote will be used for collecting and organizing course materials and can be used for general note-taking. It works on any computer, tablet, or smart phone through either an app or a web site. The coolest thing is that it automagically syncs all your notes and documents across all of your devices. The free version of Evernote is fine, and you can easily upgrade to the paid version later, if you want to. #Get a Twitter account (free), if you don't have one already. Choose a user name that is not too embarrassing, since this is professional stuff and your contributions will be visible to anyone on the web, including your grandmother and future employers (I am @JohnBTV on Twitter). If you have any privacy issues, have recently escaped from prison, or are enrolled in the Witness Protection Program, please speak to me and we'll do whatever is necessary. Make a link for #uvmgg, as all of our class tweets will go there. #Get a Wikia account (free). This will be used for hosting and editing the class wiki site (which you are reading right now). I chose Wikia, because it runs on the same software as Wikipedia (aka The World's Most Important Web Site), so you will be able to transfer all of your editing talents to Wikipedia later on. Again, be judicious with your choice of user name, since your posts, comments and edits will be public. There is a growing trend for scientists to edit Wikipedia using their real names, and to freely disclose their professional affiliations. I do this, editing both Wikipedia and Wikia as John Mackenzie Burke, but you should feel free to use anything you're comfortable with. #Download and install the free version of Geneious. Absolutely wonderful sequence analysis software that runs on Mac, PC, or Linux. Even the free version has terrific capabilities. Expectations General class requirements #Attend class regularly and be an active and constructive participant. #Read the textbook. The whole damn thing by the end of the semester. #Follow the #uvmgg Twitter feed and contribute to the discussion in a lively and constructive manner. #Add new wiki pages, content, criticisms, suggestions and edits to the required Wiki content sections (see below). Do the same in any of the optional sections, as you wish. #Be prepared to present and discuss the pages that you have contributed to in class. #Be willing to contribute your expertise to support other class members when they need it. #Become a skilled practitioner of the art of collaboration, including constructive criticism. #Learn to formulate insightful questions in the area of genetics and genomics. Required Wiki content sections #Class Notes #'Concepts and Jargon''' #Genetic Studies #Genomic Studies #Metagenomic Studies #Online Resources (databases, web sites, blogs, Twitter feeds) #Personal pages #Student-generated questions and proposed solutions #Textbook problems and solutions #YFG: Your Favorite Gene #Wikipedia page evaluations Optional Wiki content sections #Biographies of Geneticists and Genome Scientists #Books, Films and Video Reviews #Current News Evaluations #Humor for Gene Geeks #Textbook issues, corrections and updates 'WIKI CONTENT (required sections)' Class Notes | 2012 27 August | 2012 29 August | Concepts and Jargon | Allele | Alternative splicing | Annotation | Assembly | Biochemistry | Biodiversity | Bioinformatics | Biopunk | BLAST | Cancer genome | Candidate gene study | Chloroplast DNA| Classical Genetics | Clone | Combinatorial | Common ancestor | Complementation | Complex phenotypes | Contig | Copy number variation | Curation | Deletion mapping | De novo sequencing | Diploid | DIY biology | Dominance | Duplex | Enrichment | Epigenetics | Epistasis | EST | Forward genetics | Fusion | Gene | Gene chip | Gene cluster | Gene duplication | Gene synthesis | Gene therapy | Genetic counseling | Genetic drift | Genetic information | Genetic map | Genetics | Genome | Genome browser | Genomics | Genotype | GFP | GMO | GWAS | Haploid | Haplotype | High-throughput sequencing | Homolog | Huntington's disease | Indel | In vitro selection | Karyotype | Knockout | Knock-in | Lateral gene transfer | Linkage disequilibrium | Marker | Mating | Metagenome | Microarray | Mitochondrial DNA | Missing heritability | Mobile genetic element | Model organism | Molecular cloning | Mosaic | Mutagen | Mutant | Mutation | ncRNA | Null mutation | Next-gen sequencing | Noncoding | Nonsense mutation | Nucleic acid | Null mutant | Oligonucleotide | Ortholog | Paralog | Partial diploid | Personal genomics | Phenotype | Physical map | Plasmid | Polar mutation | Protein | Proteome | Pseudogene | Read | Read length | Recombination | Resequencing | Reverse genetics | Reverse transcription | RNA editing | RNA interference | RNA-seq | Screening | Selection | Selective pressure | Sexual reproduction | Sickle cell disease | Silencing | Site-directed mutagenesis | SNP | Species | Synthetic biology | Trait | Transgene | Transgenic organism | Trinucleotide repeat | Wild-type | Wreck-and-check | Yeast two-hybrid | Genetic Studies Genomic Studies Metagenomic Studies Online Resources (databases, web sites, blogs, Twitter feeds) | Belly Button Biodiversity | CDC Genomics and Health Impact Blog | Genomes Unzipped | The Genographic Project | The Personal Genome | Personal Pages Student-Generated Questions and Proposed Solutions Textbook Problems and Solutions YFG: Your Favorite Gene Wikipedia Page Evaluations 'WIKI CONTENT (optional sections)' Biographies of Geneticists and Genome Scientists | Church, George | Crick, Francis | Francklin, Rosalind | Guthrie, Christine | Lander, Eric | McClintock, Barbara | Sanger, Fred | Steitz, Joan | Thornton, Janet | Venter, Craig | Watson, James | Book, Film and Video Reviews | GATTACA (film) | Genome: The Autobiography of a Species in 23 Chapters, Ridley | Jurassic Park, Crichton | The Eighth Day of Creation, Judson | The Windup Girl, Bacigalupi | Current News Evaluations Humor For Genetics Geeks Textbook Issues, Corrections and Updates Updates, news, plans, questions and announcements Latest activity Category:Browse